PANDORA

PANDORA analyzes sets of genes, proteins, or proteolytic peptides to map them to protein sequences and derive biological meaning through integrated annotations and statistical enrichment.

Key Features:

• Mapping and Annotation Integration: Maps input gene or protein sets to corresponding protein sequences and constructs a graph-based hierarchy that elucidates relationships among biological subsets using integrated annotations.
• Extensive Annotation Resources: Integrates annotations from Gene Ontology (GO), UniProt Keywords, InterPro, Enzyme, SCOP, CATH, Gene-3D, and NCBI taxonomy, comprising ~200,000 distinct annotation terms linked to ~3.2 million sequences from the UniProt Knowledgebase (UniProtKB).
• Statistical Analysis: Performs enrichment analysis using a binomial approximation of the hypergeometric distribution with multiple hypothesis testing corrections and support for various background sets, including major gene-expression DNA-chip platforms.
• Visualization of Properties: Visualizes standard and user-defined binary and quantitative properties in conjunction with protein data.

Scientific Applications:

• Genomic research: Interprets gene sets from gene expression experiments to identify enriched biological annotations and relationships.
• Proteomic research: Analyzes proteolytic peptides and mass spectrometry (MS) proteomics datasets by mapping peptides to protein sequences and associated annotations.
• Homology and sequence-based analyses: Interprets results from BLAST searches and homology-based classifications by integrating sequence annotations and enrichment statistics.
• Functional genomics, systems biology, and personalized medicine: Supports identification of significant biological patterns and relationships within gene or protein sets relevant to these fields.

Methodology:

PANDORA maps input genes/proteins to protein sequences, constructs a graph-based hierarchy based on integrated annotations, conducts enrichment analysis using a binomial approximation of the hypergeometric distribution with multiple hypothesis testing corrections and configurable background sets (including DNA-chip platforms), and provides visualization of binary and quantitative properties.